RetrogeneDB ID: retro_itri_333

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:11452329..11453061(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025429
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VASP
• Ensembl ID: ENSSTOG00000027705
• Aliases: None
• Description: vasodilator-stimulated phosphoprotein [Source:HGNC Symbol;Acc:12652]

Sequence

>retro_itri_333
GAGGAGGTGGAGCAGCAGAAAAGGCAGTGGCCCAGCCAGCCCGAGGAAGTGGAGAGGAAGGGATGGGTCACCAAGGCAGG
AAGCCCACCTGTTCACCCAGTGGGGGGACCACCCCCGCCTCCAGGACCTCCCTGTCCTCCGGGTCCCTCCGCACCCCCAG
GATTGCCCTCCTCAGGGGTCCTGGCTTCAAGGCATGGAGTAGGGGGAGGCACATCTCCTGCGATCCCTCTCTCTGCAGCA
CAAGGATGGAATGGTGGAGATGCAGGAGCCCCTGGCTTGGCTGCAGCCATTTGGGGAGCCAAACTTAGAAAAGTCAACAA
GCAGAAGGAGACCTCAGGAAGACCGCTGGGCCCCAAAGCTGAGAACAGTCGAAGCACCGGTCCAGGGTTCATGGAGGAGA
TGGCTGCCTTGCTGGCCCAGAGAAGAAAAGCCACACAGATTGGAGGGAAACCCAAGGAAGAATCTGCTAGTCAGGAGGAG
CCAGGGGCCAGAGGCCCAGCCCAGAGTGAACCTGTGCCAAGACCCTGGGAGAAGAACAGCACAGCCTTGCTGAGGATGAA
GTCCTCTTCTTCGAGGACTGCTTCCAAGGCCCAGCCCTCCAGCCATGGGGAAGAGTCAGACCTGGAGAGGGTGAAAAGGG
AGCTTCTGGAAGAGGTGAGGAAGGAATTACAGAAGGTTAAAGAGGAGATAATTGAAGCCCTTGTCCAGGAGCTGAGGAAT
TGGGGTTCCCCC

Alignment

ORF - retro_itri_333 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 64.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEVEQQKRQQPSQPEYMERERRVSNAGGPPVPPVGGPPPPPGPPPPPGPPPPPGLPPSGVSAAGHGAGGG
          EEVEQQKRQ.PSQPE..ER...V..AG.PPV.PVGGPPPPPGPP.PPGP..PPGLP.SGV.A..HG.GGG
Retrocopy EEVEQQKRQWPSQPEEVERKGWVTKAGSPPVHPVGGPPPPPGPPCPPGPSAPPGLPSSGVLASRHGVGGG

Parental  PPPAPPLPAAQGPSGGGAGAPGLAAAIAGAKLRKVSKQEEASGGPLAAKAESTRSTGGGLMEEMNAMLAR
          ..PA.PL.AAQG..GG.AGAPGLAAAI.GAKLRKV.KQ.E.SG.PL..KAE..RSTG.G.MEEM.A.LA.
Retrocopy TSPAIPLSAAQGWNGGDAGAPGLAAAIWGAKLRKVNKQKETSGRPLGPKAENSRSTGPGFMEEMAALLAQ

Parental  RRKATQVGEKPPKEESASQEEPEARVPAQSEPVRRPWEKNSTTLPRMKSSSSITASEAQPSTHSSGEESD
          RRKATQ.G.K.PKEESASQEEP.AR.PAQSEPV.RPWEKNST.L.RMKSSSS.TAS.AQPS.H..GEESD
Retrocopy RRKATQIGGK-PKEESASQEEPGARGPAQSEPVPRPWEKNSTALLRMKSSSSRTASKAQPSSH--GEESD

Parental  LEKVKQELLEEVRKELQKVKEEIIEAFVQELRKRGSP
          LE.VK.ELLEEVRKELQKVKEEIIEA.VQELR..GSP
Retrocopy LERVKRELLEEVRKELQKVKEEIIEALVQELRNWGSP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_333 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_333 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012536	1 retrocopy	retro_cjac_184,
Ictidomys tridecemlineatus	ENSSTOG00000027705	1 retrocopy	retro_itri_333 ,